Anti-ceramide antibodies

ABSTRACT

Monoclonal antibodies directed to ceramide that inhibit apoptosis are disclosed. Humanized and scFv versions of the antibodies are also disclosed. Methods for prevention or treatment of apoptosis in a subject by administration of the anti-ceramide antibodies are disclosed.

CROSS-REFERENCE TO PRIOR APPLICATIONS

This application is a continuation of U.S. patent application Ser. No. 16/568,152, filed Sep. 11, 2019, now U.S. Pat. No. 11,447,572, which is a divisional of U.S. patent application Ser. No. 15/502,162, filed Feb. 6, 2017, now U.S. Pat. No. 10,450,385, which is a National Stage Application of PCT/US2015/044144, filed Aug. 7, 2015, which claims the benefit of and priority to U.S. Provisional Application No. 62/034,453, filed Aug. 7, 2014.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. Said XML copy, created on Sep. 30, 2022, is named 115872-1001 SL.xml and is 61,903 bytes in size.

FIELD

This application generally relates to antibodies that inhibit cell death. In particular, the invention relates to inhibition of cell death with antibodies directed to ceramide.

BACKGROUND

Acute Radiation Syndrome (ARS) (sometimes known as radiation toxicity or radiation sickness) is an acute illness caused by irradiation of a large portion of the body by a high dose of penetrating radiation; such as high energy X-rays, gamma rays, and neutrons; in a very short period of time, for example, within a matter of minutes. The major cause of this syndrome is depletion of immature parenchymal stem cells in specific tissues. Examples of people who suffered from ARS are the survivors of the Hiroshima and Nagasaki atomic bombs, the firefighters that first responded after the Chernobyl Nuclear Power Plant event in 1986, and some unintentional exposures to sterilization irradiators. In general, the radiation dose for the induction of ARS is large (i.e., greater than 0.7 Gray (Gy) or 70 rads), although mild symptoms may be observed with doses as low as 0.3 Gy or 30 rads.

Radiation gastrointestinal (GI) syndrome will usually occur with a dose greater than approximately 10 Gy (1000 rads) although some symptoms may occur as low as 6 Gy or 600 rads. Survival is extremely unlikely with this syndrome due to the destructive and irreparable changes in the GI tract and bone marrow. Radiation GI Syndrome typically can be divided into three stages. The prodromal stage manifests within several hours after exposure and symptoms include anorexia, severe nausea, vomiting, cramps, and diarrhea. The latent stage begins after about two days and the patient may appear and feel well, however, cells lining the GI tract, as well as stem cells in the bone marrow, are dying. Less than one week after exposure, the manifest illness stage begins, with symptoms including malaise, anorexia, severe diarrhea, fever, dehydration, and electrolyte imbalance. Death usually occurs within 2 weeks as a result of infection, dehydration, and electrolyte imbalance.

In addition to the treatment of acute radiation syndrome, bone marrow transplantation is currently used to treat a number of malignant and non-malignant diseases including acute and chronic leukemias, myelomas, solid tumors. However, bone marrow transplantation frequently evokes a variety of immune responses in the host, which results in rejection of the graft or graft-versus-host disease (hereinafter, referred to as “GvHD”). The conditioning regimen required prior to transplantation, designed to ablate or suppress the patient's immune system, renders the patient susceptible to neoplastic relapse or infection. Recent use of unrelated and HLA non-identical donors has unfortunately increased the incidence of GvHD. While removal of T cells from the donor marrow graft ameliorates GvHD, this strategy increases graft failure rates and markedly diminishes the therapeutically-beneficial graft-versus-tumor effect. As such, overall survival does not improve. Further, despite strong pre-clinical data, attempts to improve GvHD outcomes by diminishing inflammatory cytokine action by adding TNF antagonists to corticosteroids, the standard of care for acute GvHD, has provided limited therapeutic benefit.

Thus, there is an urgent need for alternative strategies to reduce the incidence and severity of Radiation GI Syndrome and GvHD.

SUMMARY

One aspect of the present application is directed to an anti-ceramide antibody, or an antigen-binding fragment thereof, comprising: a heavy chain variable region CDR1 of 10 amino acids comprising a Gly in the 1st position from the N-terminal, a Tyr or Phe in the 2nd position from the N-terminal, a Phe or Leu in the 4th position from the N-terminal, and a Thr or His in the 6th position from the N-terminal and a His or Asn in the 10th position from the N-terminal; a heavy chain variable region CDR2 of 16-17 amino acids comprising a Asn or Ile in the 2nd position from the N-terminal, a Phe or Ser in the 4th position from the N-terminal, a Thr in the 9th position from the C-terminal, a Tyr in the 7th position from the C-terminal, an Asn in the 6th position from the C-terminal, a Lys or Ala in the 2nd and 4th positions from the C-terminal; a heavy chain variable region CDR3 of 7 to 11 amino acids comprising a Tyr or Thr at the 4th position from the N-terminal; a light chain variable region CDR1 of 10-16 amino acids comprising an Ala or Ser in the 2nd position from the N-terminal, a Ser in the 3rd position from the N-terminal, a Ser or Asp in the 5th position from the N-terminal, and a Tyr, Ser or Phe in the 3th position from the C-terminal; a light chain variable region CDR2 of 7 amino acids comprising a Ser or Asn in the 3rd position from the N-terminal, a Lys or Ser in the 5th position from the N-terminal and a Ser or Asp in the 7th position from the N-terminal; and a light chain variable region CDR3 of 9 amino acids comprising a Gln, Leu or Trp in the 1st position from the N-terminal, a Gln in the 2nd position from the N-terminal, a Pro in the 7th position from the N-terminal and a Thr in the 9th position from the N-terminal.

Another aspect of the present application is directed to an anti-ceramide single-chain variable fragment (scFv) that binds to the same antigenic determinant as the anti-ceramide antibody of the present application. The scFv comprises: a heavy chain variable region CDR1 of 10 amino acids comprising a Gly in the 1st position from the N-terminal, a Tyr or Phe in the 2nd position from the N-terminal, a Phe or Leu in the 4th position from the N-terminal, and a Thr or His in the 6th position from the N-terminal and a His or Asn in the 10th position from the N-terminal; a heavy chain variable region CDR2 of 16-17 amino acids comprising an Asn or Ile in the 2nd position from the N-terminal, a Phe or Ser in the 4th position from the N-terminal, a Thr in the 9th position from the C-terminal, a Tyr in the 7th position from the C-terminal, an Asn in the 6th position from the C-terminal, a Lys or Ala in the 2nd and 4th positions from the C-terminal; a heavy chain variable region CDR3 of 7 to 11 amino acids comprising a Tyr or Thr at the 4th position from the N-terminal; a light chain variable region CDR1 of 10-16 amino acids comprising an Ala or Ser in the 2nd position from the N-terminal, a Ser in the 3rd position from the N-terminal, a Ser or Asp in the 5th position from the N-terminal, and a Tyr, Ser or Phe in the 3th position from the C-terminal; a light chain variable region CDR2 of 7 amino acids comprising a Ser or Asn in the 3rd position from the N-terminal, a Lys or Ser in the 5th position from the N-terminal and a Ser or Asp in the 7th position from the N-terminal; and a light chain variable region CDR3 of 9 amino acids comprising a Gln, Leu or Trp in the 1st position from the N-terminal, a Gln in the 2nd position from the N-terminal, a Pro in the 7th position from the N-terminal and a Thr in the 9th position from the N-terminal.

Another aspect of the present application is directed to a method of inhibiting cell death in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of the anti-ceramide antibody or an anti-ceramide antibody fragment of the present application.

Yet another aspect of the present application is directed to a method of treating Radiation GI Syndrome or ameliorating a symptom of Radiation GI Syndrome in a subject, comprising administering to the subject a therapeutically effective amount of the anti-ceramide antibody or an anti-ceramide antibody fragment of the present application.

Still another aspect of the present application relates to a method for the mitigation of cell death in GI syndrome in a subject in need thereof. The method comprises administration of an effective amount of an anti-ceramide antibody, or antigen binding fragment thereof, after exposure of said subject to penetrating radiation.

Still another aspect of the present invention relates to a method for the inhibition of apoptosis in GvHD in a subject in need thereof. The method comprises administration of an effective amount of an anti-ceramide antibody, or antigen binding fragment thereof, before said subject receives a transplant or after said subject receives a transplant, but before the onset of GvHD. In another aspect of the present invention, said transplant is a bone marrow transplant.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings illustrate one or more embodiments of the present disclosure and, together with the written description, serve to explain the principles of exemplary embodiments of the present disclosure.

FIGS. 1A-B show: (A) the variable heavy (VH) and light chain (VL) sequences of mAb 2A2 (SEQ ID NOS 39-40, respectively, in order of appearance), and (B) amino acid sequence alignment of 2A2 clone and human germline sequence (SEQ ID NOS 39, and 41-43, respectively, in order of appearance).

FIGS. 2A-B show: (A) humanized 2A2 heavy chain sequence (SEQ ID NOS 44-45, respectively, in order of appearance), and (B) humanized 2A2 light chain sequence (SEQ ID NOS 46-47, respectively, in order of appearance).

FIG. 3 is an illustration of a biological activity for h2A2, 9H10, 9H11, 7B10, 9A2, 6B5, and 6C8 in vitro using crude supernatant.

FIG. 4 is an illustration of an exemplary inhibition with purified antibody of Jurkat cell apoptosis, 10 Gy.

FIG. 5 is an illustration of an exemplary inhibition of crypt lethality using humanized 2a2 and murine 7B10, 6c8 and 6b5.

FIG. 6 is an illustration of exemplary sequences of mouse antibodies 6B5 (SEQ ID NOS 48 and 8, respectively, in order of appearance), 6C8 (SEQ ID NOS 15 and 51, respectively, in order of appearance), 7B10 (SEQ ID NOS 23-24, respectively, in order of appearance), 9H10 (SEQ ID NOS 49 and 32, respectively, in order of appearance), 9H11 (SEQ ID NOS 23-24, respectively, in order of appearance), 2A2 (SEQ ID NOS 39-40, respectively, in order of appearance) and humanized 2A2 antibody (h2A2) (SEQ ID NOS 50 and 43, respectively, in order of appearance), as well as depiction of an anti-ceramide consensus sequence. The alignment and consensus sequence are generated using the computer program MUSCLE multiple sequence alignment. Conservation is visualised on the alignment or a sequence group as a histogram giving the score for each column. Conserved columns are indicated by “*” (score of 11 with default amino acid property grouping), and columns with mutations where all properties are conserved are marked with a “+” (score of 10, indicating all properties are conserved). “-” means a gap.

FIG. 7 is an illustration of an exemplary 6B5 scFv inhibition of Jurkat cell apoptosis in vitro.

FIG. 8 is an illustration of an exemplary 6B5 scFv protection against GI crypt depletion in vivo when administered prior to exposure.

FIG. 9 is an illustration of an exemplary 6B5 scFv mitigation against GI crypt depletion in vivo when administered after exposure.

FIG. 10 is an illustration that anti-ceramide scFv protects intestinal crypts in a dose-dependent manner. C57BL/6 mice were administered humanized anti-ceramide 2A2 (0-1000 micrograms/mouse) or recombinant anti-ceramide scFv 6B5 (0-100 micrograms per mouse) via intravenous injection 15 min prior to 15 Gy total-body irradiation (TBI). Mice were euthanized 3.5 days following TBI, and a section of proximal jejunum was removed, cut into 3 15 mm segments, and placed in 4% paraformaldehyde. Proximal jejunum segments were cross-sectioned, mounted and slides were H&E stained prior to quantification of surviving crypts according to the method of Withers and Elkind (1970). As the intestinal crypt is the site of the intestinal stem cell, the microcolony assay is commonly used as a surrogate for intestinal stem cell survival. N=5 mice per group.

FIG. 11 is an illustration that anti-ceramide scFv retains efficacy when administered via alternative injections. C57BL/6 mice were administered humanized 2A2 anti-ceramide antibody (50 mg/kg) via intravenous (IV), intraperitoneal (IP) or subcutaneous (SC) injection 15 min prior to exposure to 15 Gy total-body irradiation. Alternatively, mice were administered 7.5 mg/kg anti-ceramide scFv 6B5 via IV, IP, SC or intramuscular (IM) injection 15 min prior to 15 Gy total-body irradiation (TBI). Mice were euthanized 3.5 days following TBI, and a section of proximal jejunum was removed, cut into 3 15 mm segments, and placed in 4% paraformaldehyde. Proximal jejunum segments were cross-sectioned, mounted and slides were H&E stained prior to quantification of surviving crypts according to the method of Withers and Elkind (1970). As the intestinal crypt is the site of the intestinal stem cell, the microcolony assay is commonly used as a surrogate for intestinal stem cell survival. N=5 mice per group.

FIG. 12 is an illustration that anti-ceramide h2a2 and scFv protect and mitigate the lethal effects of Radiation GI Syndrome. (left panel) C57BL/6 mice were administered humanized anti-ceramide 2A2 (1000 micrograms/mouse) via intravenous injection or recombinant anti-ceramide scFv 6B5 (100 micrograms per mouse) via subcutaneous injection 15 min prior to 14.5 Gy total-body irradiation (TBI). Mice received 5×106 autologous bone marrow cells 16 hours post TBI and were monitored daily for morbidity and mortality. Mice considered moribund were euthanized immediately. Data represents a Kaplan-Meier survival plot analyzed by Log-rank test. P<0.05 for both h2A2 and scFv groups vs. saline control. (right panel). Experiment was performed exactly as in left panel, except humanized anti-ceramide 2A2 (1000 micrograms/mouse) via intravenous injection or recombinant anti-ceramide scFv 6B5 (100 micrograms per mouse) via subcutaneous injection were administered 24 hours post 14.5 Gy total-body irradiation (TBI). N=5 mice per group. P<0.05 for both h2A2 and scFv groups vs. saline control.

FIG. 13 is an illustration that anti-ceramide scFv protects mice from lethal acute graft-versus-host disease. C57BL/6 mice (MHC H2^(b) haplotype) were administered PBS or 7.5 mg/kg anti-ceramide scFv 6B5 via intravenous injection 15 min prior to 1100 cGy split-dose total-body irradiation (TBI). Mice received an allogeneic bone marrow transplantation 16-20 hours post TBI consisting of 5×10⁶ bone marrow (BM) or BM and 2×10⁶ CD5+ naïve T cells from B10.BR donor mice (MHC H2^(k2) haplotype). Mice received PBS or 7.5 mg/kg anti-ceramide scFv 6B5 on days 4, 8, 12 and 16. Mice were scored weekly for GvHD-associated morbidity, including weight loss, skin lesions, fur ruffling and loss and kyphosis, and monitored for survival. Data represents a Kaplan-Meier survival plot analyzed by Log-rank test. P<0.05 for scFv group vs. saline control.

FIG. 14 is an illustration that anti-ceramide scFv protects mouse intestinal stem cells during lethal acute graft-versus-host disease. C57BL/6 mice (MHC H2^(b) haplotype) were administered PBS, 50 mg/kg humanized h2A2 antibody or 7.5 mg/kg anti-ceramide scFv 6B5 via intravenous injection 15 min prior to 1100 cGy split-dose total-body irradiation (TBI). Mice received an allogeneic bone marrow transplantation 16-20 hours post TBI consisting of 5×106 bone marrow (BM) or BM and 2×10⁶ CD5+ naïve T cells from B10.BR donor mice (MHC H2^(k2) haplotype). Mice received PBS or 7.5 mg/kg anti-ceramide scFv 6B5 on days 4 and 8. Mice were euthanized day 10 post transplant, and a section of proximal jejunum was removed, cut into 3 15 mm segments, and placed in 4% paraformaldehyde. Proximal jejunum segments were cross-sectioned, mounted and slides were H&E stained prior to quantification of surviving crypts according to the method of Withers and Elkind (1970). As the intestinal crypt is the site of the intestinal stem cell, the microcolony assay is commonly used as a surrogate for intestinal stem cell survival. N=5 mice per group.

FIG. 15 is an illustration that anti-ceramide h2A2 and scFv increase retention of CD4+ and CD8+ lymphocytes within the mesentery lymph nodes. C57BL/6 mice (MHC H2^(b) haplotype) were administered PBS, 50 mg/kg humanized h2A2 antibody or 7.5 mg/kg anti-ceramide scFv 6B5 via intravenous injection 15 min prior to 1100 cGy split-dose total-body irradiation (TBI). Mice received an allogeneic bone marrow transplantation 16-20 hours post TBI consisting of 5×10⁶ bone marrow (BM only) or BM and 2×10⁶ CDS+ naïve T cells from B10.BR donor mice (MHC H2k2 haplotype). Mice subsequently received PBS, h2A2 or scFv 6B5 on days 4 and 8. Mice were euthanized day 10 post transplant, and mesentery lymph nodes wee analyzed by flow cytometry. Data represents the total number of CD4+ and CD8+ cells from the total donor (H2^(k2) haplotype positive) CD45+ lymphocyte pool. N=5 mice per group.

DETAILED DESCRIPTION

The following detailed description is presented to enable any person skilled in the art to make and use the invention. For purposes of explanation, specific nomenclature is set forth to provide a thorough understanding of the present invention. However, it will be apparent to one skilled in the art that these specific details are not required to practice the invention. Descriptions of specific applications are provided only as representative examples. The present invention is not intended to be limited to the embodiments shown, but is to be accorded the widest possible scope consistent with the principles and features disclosed herein.

A “therapeutically effective amount,” as used herein, refers to an amount of a compound is an amount that achieves the desired biologic or therapeutic effect, namely an amount that prevents, reduces or ameliorates one or more symptoms of the enumerated diseases being treated or prevented.

The terms “treat,” “treating” or “treatment” as used herein, refers to a method of alleviating or abrogating a disorder and/or its attendant symptoms. The terms “prevent,” “preventing” or “prevention,” as used herein, refer to a method of barring a subject from acquiring a disorder and/or its attendant symptoms. In certain embodiments, the terms “prevent,” “preventing” or “prevention” refer to a method of reducing the risk of acquiring a disorder and/or its attendant symptoms.

As used herein, the terms “mitigate,” “mitigation” and “mitigating,” in regard to a treatment, refer to the treatment of an acute event after the occurrence of said event, for example, mitigating radiation damage 24 hours post exposure.

Similarly, as used herein, the terms “protect,” “protection” and “protecting,” in regard to a treatment, refer to the prophylactic administration of a therapeutic agent for the prevention or inhibition of an event prior to the occurrence of said event.

As used herein, the term “antibody” refers to immunoglobulin molecules and immunologically active portions of immunoglobulin (Ig) molecules, i.e., molecules that contain an antigen binding site that specifically binds (immunoreacts with) an antigen. The term “antibody” is used in the broadest sense and specifically covers monoclonal antibodies (including full length monoclonal antibodies), polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), recombinant antibodies, such as scFv, and antibody fragments so long as they exhibit the desired biological activity. By “specifically bind” or “immunoreacts with” is meant that the antibody reacts with one or more antigenic determinants of the desired antigen and does not react (i.e., bind) with other antigens, including polypeptides and lipids or binds at much lower affinity with other antigens.

The term “antibody” also includes antibody fragments that comprise a portion of a full length antibody, generally the antigen binding or variable region thereof. Examples of antibody fragments include Fab, Fab′, F(ab′)2, and Fv fragments; diabodies; linear antibodies; single-chain variable fragment (scFv); and multispecific antibodies formed from antibody fragments. In certain embodiments of the invention, an antibody fragment, rather than an intact antibody, is used to increase tissue penetration or tumor penetration. In other embodiments, antibody fragment are further modified to increase its serum half-life.

The term “monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. The monoclonal antibodies herein specifically include “chimeric” antibodies in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity.

“Humanized” forms of non-human antibodies are chimeric antibodies which contain minimal sequence derived from non-human immunoglobulin. For the most part, humanized antibodies are human immunoglobulins (recipient antibody) in which residues from a hypervariable region of the recipient are replaced by residues from a hypervariable region of a non-human species (donor antibody) such as mouse, rat, rabbit or nonhuman primate having the desired specificity, affinity, and/or capacity. Methods for making humanized and other chimeric antibodies are known in the art.

“Bispecific antibodies” are antibodies that have binding specificities for at least two different antigens. Methods for making bispecific antibodies are known in the art.

The use of “heteroconjugate antibodies” is also within the scope of the present invention. Heteroconjugate antibodies are composed of two covalently joined antibodies. Such antibodies have, for example, been proposed to target immune system cells to unwanted cells (U.S. Pat. No. 4,676,980). It is contemplated that the antibodies can be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosslinking agents.

As used herein, the term “LD5o” refers to “Lethal Dose, 50%” or “median lethal dose” and is the amount of a substance required to kill 50% of a test population.

Extracellular Ceramide is Required for Radiation-Induced Apoptosis

Lipid rafts, which are distinct plasma membrane microdomains comprised of cholesterol tightly associated with sphingolipids, in particular sphingomyelin, creating a liquid-ordered domain within the liquid-disordered bulk plasma membrane. Rafts differ in their protein and lipid composition from the surrounding membrane, housing signaling molecules including multiple glycosylphosphatidylinositol (GPI)-anchored proteins, doubly-acylated tyrosine kinases of the Src family and transmembrane proteins. In addition, rafts serve as sites that multiple receptors translocate into or out of upon their activation, including the B cell receptor (BCR) upon encountering antigen. Evidence suggests that these translocation events are crucial for multiple signal transduction cascades.

Sphingolipids are structural components of cell membranes and important regulators of signal transduction through the generation of ceramide. C16 ceramide has important roles in differentiation, proliferation and growth arrest. It is also an essential component of apoptotic signaling. Ceramide generation has been identified as requisite for multiple cytokine-, virus/pathogen-, environmental stress-, and chemotherapeutic-induced apoptotic events. In addition, Ceramide-rich regions on the plasma membrane of target cells are critical for sensitivity to cytotoxic T lymphocyte (CTL)-induced cell death.

Treatment and Prevention of the Lethal GI Syndrome

Cycling crypt base columnar (CBC) cells located at positions 1-3 from the bottom of the crypt of Lieberkuhn, have recently been defined as a population of intestinal stem cells. This group of cells proliferates and differentiates incessantly, replenishing the physiologic loss of enterocytes and other differentiated epithelial cells from the villus apex, thus maintaining the anatomical and functional integrity of the mucosa. A complete or near-complete depletion of this compartment appears required to permanently destroy the crypt-villus unit, while surviving stem cell clonogens, albeit even one per crypt, are capable of regenerating a fully functional crypt.

Radiation targets both the gastrointestinal microvasculature and intestinal stem cell compartments. Dysfunction of the microvascular endothelium, detected as apoptosis at four hours following radiation, represents a principle lesion leading to the GI syndrome. Endothelial dysfunction converts lesions to CBCs from sublethal to lethal, resulting in loss of regenerative crypts and promoting GI toxicity. Immunohistochemical and labeling studies with [³H]TdR and BrdUrd revealed that crypt stem cell death does not occur acutely after radiation exposure. Rather, the earliest detectable response is a temporary dose-dependent delay in progression through a late S-phase checkpoint and mitotic arrest, apparently signaled by radiation-induced DNA double strand breaks (dsb). A rapid apoptotic death occurs in growth arrested cells during the first 24 hours post irradiation that, at 12 Gy, equals 33% of the total death. In mammalian cells, DNA dsbs activate pathways of DNA damage recognition and repair, and a coordinated regulation of cell cycle checkpoint activity. The intestinal stem cell mitotic arrest appears to represent a regulated event in this pathway. A mitotic form of death occurs during this second 24 hours, representing 66% of overall death. No significant change in crypt number per intestinal circumference is apparent at this stage although crypt size progressively decreases due to continued normal migration of crypt transit and differentiated cells from the crypt into the epithelial lining of the villus and loss from the villus tip. Resumption of mitotic activity at 12-18 hours is associated with a rapid depletion of crypt stem cell clonogens and reduction in crypt number per circumference.

The lethality of GI stem cell clonogens is best assessed by the number of crypts surviving at 3.5 days after radiation exposure, which decreases exponentially as the dose increases (C. S. Potten and M. Loeffler, Development 110 (4), 1001 (1990), H. R. Withers, Cancer 28 (1), 75 (1971), and J. G. Maj, F. Paris, A. Haimovitz-Friedman et al., Cancer Res 63, 4338 (2003)). Crypts that contain surviving stem cells proliferate at an accelerated rate, producing typical regenerative crypts that split or bud to generate new crypts, until the intestinal mucosa regains a normal architecture. TBI experiments in several mouse models have demonstrated that the number of surviving crypt stem cells after exposure to 8-12 Gy is usually sufficient to support a complete recovery of the mucosa. At higher doses, however, massive stem cell clonogen loss may lead to a near total collapse of the crypt-villus system, mucosal denudation and animal death from the GI syndrome. The threshold dose for inducing the GI death, and the TBI dose producing 50% GI lethality (LD₅₀), appear to be strain-specific. Autopsy studies of C57BL/6 mice exposed to TBI revealed that 25% of the mice exposed to 14 Gy and 100% of those exposed 15 Gy succumbed to the GI syndrome at 6.8+/−0.99 days, predicting an LD₅₀ for GI death between 14 and 15 Gy. In contrast, the reported LD₅₀D6 (the LD₅₀ at day 6, serving as a surrogate marker for GI death) for BALB/c mice is 8.8+/−0.72 Gy, 11.7+/−0.22 Gy for BDF1 mice, 12.5+/−0.1 Gy for C3H/He mice, 14.9 Gy (95% confidence limits 13.9-16.0 Gy) for C3H/SPF mice, and 16.4+/−0.2 Gy for B6CF1 mice, indicating a strain-specific spectrum in mouse sensitivity to death from the GI syndrome. Strain variations in the sensitivity of other organs to radiation, such as the bone marrow and lung have also been reported.

Classically, penetrating radiation (IR) was thought to kill cells by direct damage to genomic DNA, causing genomic instability and resulting in reproductive cell death. Haimovitz-Friedman et al. (Cancer Res 63, 4338 (2003)) demonstrated in a nuclei-free system that apoptotic signaling can alternately be generated by the interaction of IR with cellular membranes. Ceramide mediated raft clustering is involved in IR-induced apoptosis and clonogenic cell death. It has long been accepted that the clonogenic compartment of the gastrointestinal (GI) mucosa is the specific and direct target for radiation in inducing GI damage.

One aspect of the present application is directed to an anti-ceramide antibody, or an antigen-binding fragment thereof, comprising: a heavy chain variable region CDR1 of 10 amino acids comprising a Gly in the 1st position from the N-terminal, a Tyr or Phe in the 2nd position from the N-terminal, a Phe or Leu in the 4th position from the N-terminal, and a Thr or His in the 6th position from the N-terminal and a His or Asn in the 10th position from the N-terminal; a heavy chain variable region CDR2 of 16-17 amino acids comprising a Asn or Ile in the 2nd position from the N-terminal, a Phe or Ser in the 4th position from the N-terminal, a Thr in the 9th position from the C-terminal, a Tyr in the 7th position from the C-terminal, an Asn in the 6th position from the C-terminal, a Lys or Ala in the 2nd and 4th positions from the C-terminal; a heavy chain variable region CDR3 of 7 to 11 amino acids comprising a Tyr or Thr at the 4th position from the N-terminal; a light chain variable region CDR1 of 10-16 amino acids comprising an Ala or Ser in the 2nd position from the N-terminal, a Ser in the 3rd position from the N-terminal, a Ser or Asp in the 5th position from the N-terminal, and a Tyr, Ser or Phe in the 3th position from the C-terminal; a light chain variable region CDR2 of 7 amino acids comprising a Ser or Asn in the 3rd position from the N-terminal, a Lys or Ser in the 5th position from the N-terminal and a Ser or Asp in the 7th position from the N-terminal; and a light chain variable region CDR3 of 9 amino acids comprising a Gln, Leu or Trp in the 1st position from the N-terminal, a Gln in the 2nd position from the N-terminal, a Pro in the 7th position from the N-terminal and a Thr in the 9th position from the N-terminal.

As used herein, the term “CDR” refers to the “complementarity determining region” of an immunoglobulin (antibody) molecule. CDRs are part of the variable domian in an antibody where the antibody binds to its specific antigen. CDRs are crucial to the diversity of antigen specificities generated by lymphocytes. There are three CDR per variable domain (i.e., CDR1, CDR2 and CDR3 in the variable domain of the light chain and CDR1, CDR2 and CDR3 in the variable domain of the heavy chain) for a total of 12 CDRs in an IgG molecule and 60 CDRs in an IgM molecule. Within the variable domain, CDR1 and CDR2 are found in the variable (V) region of a polypeptide chain, CDR3 shows the greatest variability as it is encoded by a recombination of the VJ in the case of a light chain region and VDJ in the case of heavy chain regions.

In some embodiments, the heavy chain variable region CDR1 of the anti-ceramide antibody, or antigen-binding fragment thereof, comprises the sequence GYTFTDHTIH (SEQ ID NO: 1), said heavy chain variable region CDR2 comprises the sequence YNYPRDGSTKYNEKFKG (SEQ ID NO: 2), a heavy chain variable region CDR3 comprising the sequence GFITTVVPSAY (SEQ ID NO: 3), said light chain variable region CDR1 comprises the sequence RASKSISKYLA (SEQ ID NO: 4), a light chain variable region CDR2 comprising the sequence SGSTLQS (SEQ ID NO: 5), and said light chain variable region CDR3 comprising the sequence QQHNEYPWT (SEQ ID NO: 6).

In further embodiments, the anti-ceramide antibody, or antigen-binding fragment thereof, comprises: a heavy chain variable region sequence comprising the sequence QVQLQQSDAELVKPGASVKISCKVSGYTFTDHTIHWMKQRPEQGLEW IGYNPRDGSTKYNEKFGKATLTDADKSSSTAYMQLNSLTSEDSAVYFCAKGFITTVV PSAYWGQGTLVTVSA (SEQ ID NO: 7), or a sequence with at least about 80%, 85%, 90% or 95% sequence identity to a heavy chain variable region sequence comprising SEQ ID NO: 7; and /or a light chain variable region sequence comprising SEQ ID NO: 8, or a sequence with at least about 80%, 85%, 90% or 95% sequence identity to a light chain variable region sequence comprising the sequence DVQITQSPSYLAASPGETITINCRASKSISKYLAWYQ EKPGKTNKLLIYSGSTLQ SGIPSRF SGSGSGTDFTLTIS SLEPEDFAMYYCQQHNEYPW TFGGGTKLEIK (SEQ ID NO: 8).

In other embodiments, the heavy chain variable region CDR1 of the anti-ceramide antibody, or antigen-binding fragment thereof, comprises the sequence GYAFSSYWMN (SEQ ID NO: 9), said heavy chain variable region CDR2 comprises the sequence QIYPGDGDTNYNGKFKG (SEQ ID NO: 10), a heavy chain variable region CDR3 comprising the sequence RCYYGLYFDV (SEQ ID NO: 11), said light chain variable region CDR1 comprises the sequence KASQDINRYLS (SEQ ID NO: 12), a light chain variable region CDR2 comprising the sequence RANRLVD (SEQ ID NO: 13), and said light chain variable region CDR3 comprising the sequence LQYDEFPYT (SEQ ID NO: 14).

In further embodiments, the anti-ceramide antibody, or antigen-binding fragment thereof, comprises: a heavy chain variable region sequence comprising the sequence

QVQLQQSGAELVKPGASVKISCKASGYAF SSYWMNWVKQRPGKGLEWIGQIYPGD GDTNYNGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCTRRCYYGLYFDVWG TGTTVTVSS (SEQ ID NO: 15), or a sequence with at least about 80%, 85%, 90% or 95% sequence identity to a heavy chain variable region sequence comprising SEQ ID NO: 15; and/or a light chain variable region sequence comprising the sequence DIKMTQSPSSRYASLG ERVTITCKASQDINRYLSWFQQKPGKSPKTLIYRANRLVDGVPSSRFSGSGSGQDYSL TISSLEYEDMGIYYCLQYDEFPYTFGGGTKLEIK (SEQ ID NO: 16), or a sequence with at least about 80%, 85%, 90% or 95% sequence identity to a light chain variable region sequence comprising SEQ ID NO: 16.

In yet other embodiments, the heavy chain variable region CDR1 of the anti-ceramide antibody, or antigen-binding fragment thereof, comprises the sequence GYTFTSYWMH (SEQ ID NO: 17), said heavy chain variable region CDR2 comprises the sequence YINPSSGYTKYNQFKD (SEQ ID NO: 18), a heavy chain variable region CDR3 comprising the sequence GGYYGFAY (SEQ ID NO: 19), said light chain variable region CDR1 comprises the sequence SASSSVSYMY(SEQ ID NO: 20), a light chain variable region CDR2 comprising the sequence LTSNLAS (SEQ ID NO: 21), and said light chain variable region CDR3 comprising the sequence QQWSSNPLT (SEQ ID NO: 22).

In further embodiments, the anti-ceramide antibody, or antigen-binding fragment thereof, comprises: a heavy chain variable region sequence comprising the sequence

QVQLQQSGAELAKPGASVKLSCKASGYTFTSYWMHWVKQRPGQGLEWIGYINPSS GYTKYNQKFKDKATLTADKSSSTAYMQLSSLTYEDSAVYYCARGGYYGFAYWGQ GTLVTVSA (SEQ ID NO: 23), or a sequence with at least about 80%, 85%, 90% or 95% sequence identity to a heavy chain variable region sequence comprising SEQ ID NO: 23; and /or a light chain variable region sequence comprising the sequence QIVLTQSPALMSASP GEKVTMTCSASSSVSYMYWYQQKPRSSPKPWIYLTSNLASGVPARFSGSGSGTSYSL TISSMEAEDAATYYCQQWSSNPLTFGAGTKLELK (SEQ ID NO: 24), or a sequence with at least about 80%, 85%, 90% or 95% sequence identity to a light chain variable region sequence comprising SEQ ID NO: 24.

In still other embodiments, the heavy chain variable region CDR1 of the anti-ceramide antibody, or antigen-binding fragment thereof, comprises the sequence GFSLTGYGVH (SEQ ID NO: 25), said heavy chain variable region CDR2 comprises the sequence VIWSGGSTDYNAAFIS (SEQ ID NO: 26), a heavy chain variable region CDR3 comprising the sequence NYGYDYAMDY (SEQ ID NO: 27), said light chain variable region CDR1 comprises the sequence RASQSIGTSIH (SEQ ID NO: 28), a light chain variable region CDR2 comprising the sequence YASESIS (SEQ ID NO: 29), and said light chain variable region CDR3 comprising the sequence QQSNSWPFT (SEQ ID NO: 30).

In further embodiments, the anti-ceramide antibody, or antigen-binding fragment thereof, comprises: a heavy chain variable region sequence comprising SEQ ID NO: 31, or a sequence with at least about 80%, 85%, 90% or 95% sequence identity to a heavy chain variable region sequence comprising the sequence

QVQLKQSGPGVQPSSLSITCTVS GFSLTSYGVHWVRQSPGKGLEWLGVIWSGGSTDYNAAFISRLSISKDNSKSQVFFKM NSLQADDTAIYYCARNYGYDYAMDYWGQGTSVTVSS (SEQ ID NO: 31); and /or a light chain variable region sequence comprising the sequence DILLTQSPAILSVSPGERVSF SCRASQSIGTSIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESED IADYYCQQSNSWPFTFGSGTKLEIK (SEQ ID NO: 32), or a sequence with at least about 80%, 85%, 90% or 95% sequence identity to a light chain variable region sequence comprising SEQ ID NO: 32.

In even other embodiments, the heavy chain variable region CDR1 of the anti-ceramide antibody, or antigen-binding fragment thereof, comprises the sequence GYTFTNYWMH (SEQ ID NO: 33), said heavy chain variable region CDR2 comprises the sequence AIYPGDSDTSYNQKFKG (SEQ ID NO: 34), a heavy chain variable region CDR3 comprising the sequence GLYYGYD (SEQ ID NO: 35), said light chain variable region CDR1 comprises the sequence KSSQSLIDSDGKTFLN (SEQ ID NO: 36), a light chain variable region CDR2 comprising the sequence LVSKLDS (SEQ ID NO: 37), and said light chain variable region CDR3 comprising the sequence WQGTHFPYT (SEQ ID NO: 38).

In further embodiments, the anti-ceramide antibody, or antigen-binding fragment thereof, comprises: a heavy chain variable region sequence comprising the sequence EVQLQQSGTVLARPGASVKMSCKASGYTFTNYWMHWVKQRPVQGLEW IGAIYPGDSDTSYNQKFKGKAKLTAVTSTSTAFMELSSLTNEDSAVYYCTGLYYGYD WGQGTTLTVSS (SEQ ID NO: 39), or a sequence with at least about 80%, 85%, 90% or 95% sequence identity to a heavy chain variable region sequence comprising SEQ ID NO: 39; and /or a light chain variable region sequence comprising SEQ ID NO: 40, or a sequence with at least about 80%, 85%, 90% or 95% sequence identity to a light chain variable region sequence comprising the sequence DVLMTQTPLTLSVTIGQPASISCKSSQSLIDSDGKTF LNWLLQRPGQSPKRLIYLVSKLDSGVPDRFTGSGSGTDFTLKISRVEAEDLGLYYCW QGTHFPYTFGGGTKLEIK (SEQ ID NO: 40).

In still yet other embodiments, the anti-ceramide antibody, or antigen-binding fragment thereof, comprises: a) a heavy chain variable region sequence comprising a sequence selected from the group consisting of SEQ ID NOs: 7, 15, 23, 31 and 39, or a sequence with at least about 80%, 85%, 90% or 95% sequence identity to a heavy chain variable region sequence comprising a sequence selected from the group consisting of SEQ ID NOs: 7, 15, 23, 31 and 39; and /or a) a light chain variable region sequence comprising a sequence selected from the group consisting of SEQ ID NOs: 8, 16, 24, 32 and 40, or a sequence with at least about 80%, 85%, 90% or 95% sequence identity to a light chain variable region sequence comprising a sequence selected from the group consisting of SEQ ID NOs: 8, 16, 24, 32 and 40.

In particular embodiments, the anti-ceramide antibody is selected from the group consisting of monoclonal antibody, chimeric antibody, humanized antibody, human antibody, recombinant antibody and scFv.

Another aspect of the present application is directed to an anti-ceramide single-chain variable fragment (scFv) that binds to the same antigenic determinant as the anti-ceramide antibody of the present application. The scFv comprises: a heavy chain variable region CDR1 of 10 amino acids comprising a Gly in the 1st position from the N-terminal, a Tyr or Phe in the 2nd position from the N-terminal, a Phe or Leu in the 4th position from the N-terminal, and a Thr or His in the 6th position from the N-terminal and a His or Asn in the 10th position from the N-terminal; a heavy chain variable region CDR2 of 16-17 amino acids comprising a Asn or Ile in the 2nd position from the N-terminal, a Phe or Ser in the 4th position from the N-terminal, a Thr in the 9th position from the C-terminal, a Tyr in the 7th position from the C-terminal, an Asn in the 6th position from the C-terminal, a Lys or Ala in the 2nd and 4th positions from the C-terminal; a heavy chain variable region CDR3 of 7 to 11 amino acids comprising a Tyr or Thr at the 4th position from the N-terminal; a light chain variable region CDR1 of 10-16 amino acids comprising an Ala or Ser in the 2nd position from the N-terminal, a Ser in the 3rd position from the N-terminal, a Ser or Asp in the 5th position from the N-terminal, and a Tyr, Ser or Phe in the 3th position from the C-terminal; a light chain variable region CDR2 of 7 amino acids comprising a Ser or Asn in the 3rd position from the N-terminal, a Lys or Ser in the 5th position from the N-terminal and a Ser or Asp in the 7th position from the N-terminal; and a light chain variable region CDR3 of 9 amino acids comprising a Gln, Leu or Trp in the 1st position from the N-terminal, a Gln in the 2nd position from the N-terminal, a Pro in the 7th position from the N-terminal and a Thr in the 9th position from the N-terminal.

A single-chain variable fragment (scFv) is not actually a fragment of an antibody, but instead is a fusion protein of the variable regions of the heavy (VH) and light chains (VL) of immunoglobulins, connected with a short linker peptide of ten to about 25 amino acids. The linker is usually rich in glycine for flexibility, as well as serine or threonine for solubility, and can either connect the N-terminus of the VH with the C-terminus of the VL, or vice versa. The scFv retains the specificity of the original immunoglobulin, despite removal of the constant regions and the introduction of the linker.

In some embodiments, the anti-ceramide antibodies, antigen-binding fragments thereof, or scFv are produced using recombinant DNA technologies. Procedures for the expression and purification of recombinant proteins are well established in the art.

In order to express the anti-ceramide antibody, antigen-binding fragment thereof, or scFv of the present application in a biological system, a polynucleotide that encodes the anti-ceramide antibody, antigen-binding fragment thereof, or scFv is constructed. In certain embodiments, the recombinant polynucleotide is codon optimized for expression in a selected prokaryotic or eukaryotic host cell, such as a bacterial, mammalian, plant or insect cell. To facilitate replication and expression, the polynucleotide can be incorporated into a vector, such as a prokaryotic or a eukaryotic expression vector. Although the polynucleotide disclosed herein can be included in any one of a variety of vectors (including, for example, bacterial plasmids; phage DNA; baculovirus; yeast plasmids; vectors derived from combinations of plasmids and phage DNA, viral DNA such as vaccinia, adenovirus, fowl pox virus, pseudorabies, adenovirus, adeno-associated virus, retroviruses and many others), most commonly the vector will be an expression vector suitable for generating polypeptide expression products. In an expression vector, the polynucleotide encoding the anti-ceramide antibody, antigen-binding fragment thereof, or scFv is typically arranged in proximity and orientation to an appropriate transcription control sequence (promoter, and optionally, one or more enhancers) to direct mRNA synthesis. That is, the polynucleotide sequence of interest is operably linked to an appropriate transcription control sequence. Examples of such promoters include: the immediate early promoter of CMV, LTR or SV40 promoter, polyhedron promoter of baculovirus, E. coli lac or trp promoter, phage T7 and lambda P_(L) promoter, and other promoters known to control expression of genes in prokaryotic or eukaryotic cells or their viruses. The expression vector typically also contains a ribosome binding site for translation initiation, and a transcription terminator. The vector optionally includes appropriate sequences for amplifying expression. In addition, the expression vectors optionally comprise one or more selectable marker genes to provide a phenotypic trait for selection of transformed host cells, such as dihydrofolate reductase or neomycin resistance for eukaryotic cell culture, or such as tetracycline or ampicillin resistance in E. coli.

The expression vector can also include additional expression elements, for example, to improve the efficiency of translation. These signals can include, e.g., an ATG initiation codon and adjacent sequences. In some cases, for example, a translation initiation codon and associated sequence elements are inserted into the appropriate expression vector simultaneously with the polynucleotide sequence of interest (e.g., a native start codon). In such cases, additional translational control signals are not required. However, in cases where only a polypeptide coding sequence, or a portion thereof, is inserted, exogenous translational control signals, including an ATG initiation codon is provided for expression of the anti-ceramide antibody or scFv. The initiation codon is placed in the correct reading frame to ensure translation of the polynucleotide sequence of interest. Exogenous transcriptional elements and initiation codons can be of various origins, both natural and synthetic. If desired, the efficiency of expression can be further increased by the inclusion of enhancers appropriate to the cell system in use.

Expression vectors carrying the anti-ceramide antibody or scFv of the present application can be introduced into host cells by any of a variety of well-known procedures, such as electroporation, liposome mediated transfection, calcium phosphate precipitation, infection, transfection and the like, depending on the selection of vectors and host cells.

Host cells that contain anti-ceramide antibody, antigen-binding fragment thereof, or scFv-encoding nucleic acids are, thus, also a feature of this disclosure. Favorable host cells include prokaryotic (i.e., bacterial) host cells, such as E. coli, as well as numerous eukaryotic host cells, including fungal (e.g., yeast, such as Saccharomyces cerevisiae and Picchia pastoris) cells, insect cells, plant cells, and mammalian cells (such as CHO cells).

The host cells can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants, or amplifying the inserted polynucleotide sequences. The culture conditions, such as temperature, pH and the like, are typically those previously used with the host cell selected for expression, and will be apparent to those skilled in the art. A host cell is optionally chosen for its ability to modulate the expression of the inserted sequences or to process the expressed protein in the desired fashion. Such modifications of the protein include, but are not limited to, glycosylation, (as well as, e.g., acetylation, carboxylation, phosphorylation, lipidation and acylation). Post-translational processing for example, which cleaves a precursor form into a mature form of the protein (for example, by a furin protease) is optionally performed in the context of the host cell. Different host cells such as 3T3, COS, CHO, HeLa, BHK, MDCK, 293, WI38, etc. have specific cellular machinery and characteristic mechanisms for such post-translational activities and can be chosen to ensure the correct modification and processing of the introduced, foreign protein.

For long-term, high-yield production of recombinant anti-ceramide antibody, antigen-binding fragment thereof, or scFv polypeptide, stable expression systems are typically used. For example, polynucleotides encoding an anti-ceramide antibody, antigen-binding fragment thereof, or scFv are introduced into the host cell using expression vectors which contain viral origins of replication or endogenous expression elements and a selectable marker gene. Following the introduction of the vector, cells are allowed to grow for 1-2 days in an enriched media before they are switched to selective media. The purpose of the selectable marker is to confer resistance to selection, and its presence allows growth and recovery of cells which successfully express the introduced sequences. For example, resistant groups or colonies of stably transformed cells can be proliferated using tissue culture techniques appropriate to the cell type. Host cells transformed with a nucleic acid encoding an anti-ceramide antibody, antigen-binding fragment thereof, or scFv are optionally cultured under conditions suitable for the expression and recovery of the encoded protein from cell culture.

Following transduction of a suitable host cell line and growth of the host cells to an appropriate cell density, the selected promoter is induced by appropriate means (e.g., temperature shift or chemical induction) and cells are cultured for an additional period. The secreted polypeptide product is then recovered from the culture medium. Alternatively, cells can be harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract retained for further purification. Eukaryotic or microbial cells employed in expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents, or other methods, which are well know to those skilled in the art.

Expressed anti-ceramide antibody, antigen-binding fragment thereof, or scFv can be recovered and purified from recombinant cell cultures by any of a number of methods well known in the art, including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography (e.g., using any of the tagging systems noted herein), hydroxylapatite chromatography, and lectin chromatography. Protein refolding steps can be used, as desired, in completing configuration of the mature protein. Finally, high performance liquid chromatography (HPLC) can be employed in the final purification steps.

In certain examples, the nucleic acids are introduced into vectors suitable for introduction and expression in prokaryotic cells, e.g., E. coli cells. In some embodiments, the expression vector is introduced (e.g., by electroporation) into a suitable bacterial host. In another example, a polynucleotide sequence that encodes an anti-ceramide antibody or scFv is introduced into insect cells using a Baculovirus Expression Vector System (BEVS). Similarly, alternative insect cells can be employed, such as SF21 which is closely related to the SF9, and the High Five (Hi5) cell line derived from a cabbage looper, Trichoplusia ni.

In yet other embodiments, the anti-ceramide antibody, antigen-binding fragment thereof, or scFv is expressed in vivo by a plasmid vector or a viral vector.

In certain embodiments, the anti-ceramide antibodies, antigen-binding fragments thereof, and scFv are produced by chemical synthesis. Briefly, an anti-ceramide antibody, antigen-binding fragment thereof, or scFv may be synthesized by coupling the carboxyl group or C-terminus of one amino acid to the amino group or N-terminus of another. Due to the possibility of unintended reactions, protecting groups may be necessary. Chemical peptide synthesis starts at the C-terminal end of the peptide and ends at the N-terminus. This is the opposite of protein biosynthesis, which starts at the N-terminal end.

In some embodiments, the anti-ceramide antibodies, antigen-binding fragments thereof, and scFv may be synthesized using traditional liquid- or solid-phase synthesis. Fmoc and t-Boc solid phase peptide synthesis (SPPS) can be employed to grow the peptides from carboxy to amino-terminus. In certain embodiments, the last “amino acid” added to the reaction is PEGylated. This last amino acid is often referred to as a carboxyl-PEG-amine, carboxyl-PEO-amine, or amine-PEG-acid, whereby the amine is blocked to protect against reaction and the acid is free to react with the amine group from the previously added amino acid in the reaction. PEG (polyethylene glycol) and PEO (polyethylene oxide) are polymers composed of repeating subunits of ethylene glycol and ethylene oxide monomers. In one embodiment, a PEGylated anti-ceramide antibody, antigen-binding fragments thereof, and scFv would have the PEG moiety connected to the histidine residue (H) at the amino-terminus of the polypeptide. In one embodiment, the PEG moiety is 5 to 30 kDa in size. In another embodiment, the PEG moiety is 10 to 20 kDa in size.

In addition to using PEGylated end amino acid during synthesis, an anti-ceramide antibody, antigen-binding fragment thereof, or scFv may be PEGylated by PEGylation. PEGylation is the process of covalent attachment of polyethylene glycol polymer chains to another molecule, normally a drug or therapeutic protein. PEGylation can be achieved by incubation of a reactive derivative of PEG with the target anti-ceramide antibody or scFv. The covalent attachment of PEG to an anti-ceramide antibody or scFv can “mask” the anti-ceramide antibody, antigen-binding fragment thereof, or scFv from the host's immune system (reduced immunogenicity and antigenicity), increase the hydrodynamic size (size in solution) of the anti-ceramide antibody, antigen-binding fragment thereof, or scFv which prolongs its circulatory time by reducing renal clearance. PEGylation can also provide water solubility to hydrophobic proteins.

Method of Inhibiting Apoptosis

Still another aspect of the present application is directed to a method of inhibiting cell death in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of an anti-ceramide antibody, or antigen-binding fragment thereof, of the present application. In some embodiments, the anti-ceramide antibody is an anti-ceramide scFv.

In some embodiments, the cell death is associated with a disease selected from the group consisting of graft versus host disease, radiation disease, GI syndrome and autoimmune disease. In some further embodiments, the disease is radiation disease or GI syndrome and the anti-ceramide antibody, or antigen-binding fragment thereof, is administered before the subject is exposed to radiation.

Another aspect of the present application is directed to a method for the mitigation of cell death in GI syndrome in a subject in need thereof. The method comprises the administration of an effective amount of an anti-ceramide antibody. In some embodiments, the method comprises administering said anti-ceramide antibody to said subject immediately after exposure of said subject to penetrating radiation. In other embodiments, the method comprises administering said anti-ceramide antibody to said subject within one hour after exposure of said subject to penetrating radiation. In still other embodiments, the method comprises administering said anti-ceramide antibody to said subject within 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or 18 hours after exposure of said subject to penetrating radiation. In a particular embodiment, the method comprises administering said anti-ceramide antibody to said subject within 24 hours after exposure of said subject to penetrating radiation. In other embodiments, the method comprises administering said anti-ceramide antibody to said subject within 30, 36, 42, 48, 54, 60, 66 or 72 hours after exposure of said subject to penetrating radiation. In other embodiments, the method comprises administering said anti-ceramide antibody to said subject within 48, 36, 24, 18, 12, 10, 8, 6, 4, 2 or 1 hour(s), or within 45, 30 or 15 minutes before exposure of said subject to penetrating radiation.

In other further embodiments, the disease is graft versus host disease and the anti-ceramide antibody, or antigen-binding fragment thereof, is administered before the subject receives a transplant. In some embodiments, the transplant is a bone marrow transplant. In still other further embodiments, the anti-ceramide antibody, or antigen-binding fragment thereof, is administered after the subject receives a transplant, but before the onset of graft versus host disease. In even still other further embodiments, the anti-ceramide antibody, or antigen-binding fragment thereof, is administered to a subject in need thereof after the onset of graft versus host disease in an amount effective for the mitigation of apoptosis in graft versus host disease.

Antibody Administration

The antibody, or antigen-binding fragment thereof, may be administered to the subject with known methods, such as intravenous administration as a bolus or by continuous infusion over a period of time, by intramuscular, intraperitoneal, intracerobrospinal, subcutaneous, intra-articular, intrasynovial, intrathecal, oral, topical, or inhalation routes.

Antibodies and antigen-binding fragments thereof of the invention can be administered in the usually accepted pharmaceutically acceptable carriers. Acceptable carriers include, but are not limited to, saline, buffered saline, glucose in saline. Solid supports, liposomes, nanoparticles, microparticles, nanospheres or microspheres may also be used as carriers for administration of the antibodies or antigen-binding fragment thereof.

The appropriate dosage (“therapeutically effective amount”) of the antibody, or antigen-binding fragment thereof, will depend, for example, on the condition to be treated, the severity and course of the condition, whether the antibody is administered for preventive or therapeutic purposes, previous therapy, the patient's clinical history and response to the antibody, the type of antibody, or antigen-binding fragment thereof, used, and the discretion of the attending physician. The antibody, or antigen-binding fragment thereof, is suitably administered to the patent at one time or over a series of treatments and may be administered to the patent at any time from diagnosis onwards. The antibody, or antigen-binding fragment thereof, may be administered as the sole treatment or in conjunction with other drugs or therapies useful in treating the condition in question.

As a general proposition, the therapeutically effective amount of the antibody, or antigen-binding fragment thereof, administered will be in the range of about 1 ng/kg body weight/day to about 100 mg/kg body weight/day whether by one or more administrations. In a particular embodiments, the range of antibody administered is from about 1 ng/kg body weight/day to about 1μg/kg body weight/day, 1 ng/kg body weight/day to about 100 ng/kg body weight/day, 1 ng/kg body weight/day to about 10 ng/kg body weight/day, 10 ng/kg body weight/day to about 1 μg/kg body weight/day, 10 ng/kg body weight/day to about 100 ng/kg body weight/day, 100 ng/kg body weight/day to about 1 μg/kg body weight/day, 100 ng/kg body weight/day to about 10 μg/kg body weight/day, 1 μg/kg body weight/day to about 10 μg/kg body weight/day, 1 μg/kg body weight/day to about 100 μg/kg body weight/day, 10 μg/kg body weight/day to about 100 μg/kg body weight/day, 10 μg/kg body weight/day to about 1 mg/kg body weight/day, 100 μg/kg body weight/day to about 10 mg/kg body weight/day, 1 mg/kg body weight/day to about 100 mg/kg body weight/day and 10 mg/kg body weight/day to about 100 mg/kg body weight/day.

In another embodiment, the antibody, or antigen-binding fragment thereof, is administered at a dosage range of 1 ng-10 ng per injection, 10 ng to100 ng per injection, 100 ng to 1 μg per injection, 1 μg to 10 μg per injection, 10 μg to 100 μg per injection, 100 μg to 1 mg per injection, 1 mg to 10 mg per injection, 10 mg to 100 mg per injection, and 100 mg to 1000 mg per injection.

In another particular embodiment, the dose range of antibody, or antigen-binding fragment thereof, administered is from about 1 ng/kg to about 100 mg/kg In still another particular embodiment, the range of antibody administered is from about 1 ng/kg to about 10 ng/kg, about 10 ng/kg to about 100 ng/kg, about 100 ng/kg to about 1 μg/kg, about 1 μg/kg to about 10 μg/kg, about 10 μg/kg to about 100 μg/kg, about 100 μg/kg to about 1 mg/kg, about 1 mg/kg to about 10 mg/kg, about 10 mg/kg to about 100 mg/kg, about 0.5 mg/kg to about 30 mg/kg, and about 1 mg/kg to about 15 mg/kg.

In other particular embodiments, the amount of antibody, or antigen-binding fragment thereof, administered is, or is about, 0.0006, 0.001, 0.003, 0.006, 0.01, 0.03, 0.06, 0.1, 0.3, 0.6, 1, 3, 6, 10, 30, 60, 100, 300, 600 and 1000 mg/day. As expected, the dosage will be dependent on the condition, size, age and condition of the patient.

The antibody, or antigen-binding fragment thereof, may be administered, as appropriate or indicated, a single dose as a bolus or by continuous infusion, or as multiple doses by bolus or by continuous infusion. Multiple doses may be administered, for example, multiple times per day, once daily, every 2, 3, 4, 5, 6 or 7 days, weekly, every 2, 3, 4, 5 or 6 weeks or monthly. However, other dosage regimens may be useful. The progress of this therapy is easily monitored by conventional techniques.

The present invention is further illustrated by the following examples which should not be construed as limiting. The contents of all references, patents and published patent applications cited throughout this application, as well as the Figures and Tables, are incorporated herein by reference.

Example 1: 2A2 Ab Humanization and Production

Cloning of variable light and heavy chain of 2A2 from hybridoma

2A2 hybridoma cells were harvested by centrifugation and total RNA was extracted from cells using RNA purification kit. This total RNA was used for cDNA synthesis and finally V-region genes of 2A2 were isolated using primer sets published in “Phage display manual”. FIG. 1A shows the variable heavy (VH) and light chain sequences (VL) of 2A2.

Humanization of 2A2 Variable Region

Usually, rodent antibodies can be immunogenic to human and cause very serious side effects including the HAMA (human anti-mouse antibodies) response or anaphylactic shock. To overcome this problem, antibody engineering has been used to humanize non-human antibodies. Therefore, the CDR grafting method was used to humanize the VL and VH of 2A2.

CDR grafting is currently the most frequently used strategy for the humanization of rodent mAbs. In this approach, CDR loops that make up the antigen-binding site of the rodent mAb are grafted into the corresponding human framework regions.

To identify human VL and VH homologous to those of 2A2, the variable regions of 2A2 were compared with variable regions of human germline sequences using the VBASE online database (vbase.mrc-cpe.cam.ac.uk). As a result, two human germline VL and VH sequences were found. Amino acid sequence alignment of 2A2 clones and human germline sequence is shown in FIG. 1B.

The selected 2A2 VH sequence was found to be most homologous to the human V gene 1-46 from the VH1 family and human J gene JH6. The selected 2A2 VL sequence was found to be most homologous with the human V gene Al from the Vk2 family and human J gene Jk2. So, synthesized VL and VH that each contained three of mouse CDR sequences were grafted into the selected human framework sequences for humanization of 2A2 mAb.

Vector Construction for the Expression of Humanized 2A2 IgG1 in Mammalian Cells

2A2 mAb is originally murine IgM. IgM antibodies are converted to the IgG1 format because IgG1 is the most abundant in serum (9 mg/ml), its half-life (21 days) is longer than any other antibodies, and, currently, most commercial therapeutic antibodies are IgG1 format. To construct humanized 2A2 IgG1 in a mammalian expression vector, pOptiVEC and pcDNA 3.3 (Invitrogen) vectors were used.

Vector for the Expression of Humanized 2A2 IgG1 in Mammalian Cells

The exemplary vector contains the human cytomegalovirus (CMV) immediate-early promoter/enhancer for high-level expression of recombinant proteins in a wide range of mammalian cells. To construction of humanized 2A2 IgG1, human variable light and heavy chain each with three CDRs of mouse 2A2 were synthesized and these two DNA fragments were linked to the human constant light and heavy chain by PCR. Finally, the humanized 2A2 light chain was cloned into pcDNA3.3 TOPO, and humanized 2A2 heavy chain was cloned into the pOptiVEC TOPO antibody expression vector. Sequences of human 2A2 IgG1 are shown in FIGS. 2A-B, which indicated that first amino acid (Arginine, red color shading) of human constant light chain was missed during construction of whole humanized light chain. After construction of these human 2A2 Ab expression vectors, the DNA plasmids were co-transfected into CHO-derived, DHFR-negative DG44 cells to create a stable cell line that produces 2A2 hIgG1 antibody.

Development of Stable Cell Lines for Antibody Production

To obtain cell lines that produce high levels of antibody, a pool of stably-transfected cells were selected by performing two rounds of selection using CD OptiCHO medium and CD OptiCHO medium with 500 μg/ml of Geneticine, followed by MTX genomic amplification selection and two rounds of single cell clonal selection in semi-solid media in a 96-well plate. Antibody expression levels were screened by ELISA assay quantification and selected h2A2IgG1-CHO cell (G3A10, C5G6 and D5F11) lines were slowly scaled up.

Example 2: Generation of Additional Anti-Ceramide Antibodies

A panel of monoclonal antibodies was generated for use in repeat-administration studies in mice to study immunogenicity. Screening of hybridomas to select anti-ceramide Mabs was performed by ELISA, using the antigen (Omega-COOH C16-ceramide coupled to albumin). Positive hits were counterscreened against both BSA and Omega-COOH C16-dihydroceramide coupled to albumin. Biologic testing of Mabs (in vitro inhibition of Jurkat cell apoptosis, in vivo inhibition of Radiation GI Syndrome) was then performed. Clones designated 9H10, 9H11, 9A2, 7B10, 6B5 and 6C8 were selected for testing and all but 9A2 demonstrated biologic activity in vitro. As shown in Table 1, a panel of clones preferentially bind C16:0 carboxyceramide-BSA. Agl is C16:0 carboxyceramide-BSA coated @ 300 ng/well, Ag2 is C-16:0 dihydro-carboxyceramide-BSA coated @ 300 ng/well and Ag3 is Free BSA (Sigma A6003) coated @ 300 ng/well.

TABLE 1 Anti-Ceramide mAbs Ag1 OD AG1 OD Ag2 OD Ag3 OD Clone # (IgG(gamma)) (IgM(Mμ)) (gamma) (gamma) 6B5 2.201 0.054 0.049 1.295 7E8 1.530 0.045 0.077 0.906 8H8 3.000 0.103 0.098 3.000 9A2 3.000 0.055 0.078 3.000 7B10 0.080 0.180 0.078 0.077 9H10 0.052 0.230 0.064 0.095 9H11 0.045 0.343 0.047 0.105 6C8 0.192 0.039 0.049 0.098 NC 0.047 0.066 0.048 0.096 PC 3.000 0.067 0.070 3.000 NC = 50% of culture media + 50% of 5% milk/PBS PC = Cardiac Serum Mouse #1 @ 1:1K

Clones 6B5 and 6C8 were identified as IgG while clones 7B10, 9H10 and 9H11 were identified as IgM. Additional data for those identified as IgG is found in Table 2. Agl is C16:0 carboxyceramide-BSA coated @ 500 ng/well in sodium bicarbonate, Ag2 is C-16:0 dihydro-carboxyceramide-BSA coated @ 500 ng/well in sodium bicarbonate and Ag3 is Free BSA (Sigma A6003) coated @ 500 ng/well in sodium bicarbonate.

TABLE 2 Concentration Curve of Anti-Ceramide mAbs Clone #/ Ag1 AG1 Ag2 Ag2 Ag3 Ag3 Ab dilution (gamma) (Mμ) (gamma) (Mμ) (gamma) (Mμ) 6B5 0.639 0.072 0.150 (0.99 mg/ml) 10 μg/ml 6B5 0.399 0.089 0.119 (0.99 mg/ml) 1 μg/ml 6B5 0.147 0.072 0.079 (0.99 mg/ml) 0.1 μg/ml 6C8 0.119 0.073 0.062 (0.79 mg/ml) 10 μg/ml 6C8 0.057 0.074 0.057 (0.79 mg/ml) 1 μg/ml 6C8 0.052 0.068 0.056 (0.79 mg/ml) 0.1 μg/ml NC 0.053 0.062 0.048 0.052 0.060 0.056 PC 1.426 0.218 0.094 0.070 0.350 0.127 NC = 5% milk-PBS PC = CERM01 Tail Bleed Serum Mouse #1 @ 1:1K

FIG. 3 shows that clones 9H10, 9H11, 7B10, 6B5 and 6C8 demonstrate biologic activity in vitro.

Positive clones were screened for biologic activity by exposing Jurkat cells to 10 Gy penetrating radiation. Monoclonal antibodies (Mabs) added to culture medium at indicated doses just prior to IR and the cells were fixed after 16 hr incubation. Apoptosis was quantified by HOESCHST bisbenzimide stain and morphologic examination. The results are shown in FIG. 4 .

Crypt lethality was studied on clones 7B10 (IgM), 6B5 (IgG), and 6C8 (IgG). FIG. 5 shows that all dose-dependently inhibited crypt lethality when administered 15 minutes prior to the 15 Gy IR.

The CDRs of 6B5, 6C8, 7B10, 9H10 and 9H11 were sequenced. Sequence data revealed significant homology amongst these Mabs, as well as with the CDRs of 2A2 (generated via an alternative immunization/screening protocol). IgMs appear to have even greater homology amongst each other and 2A2. In the same way the two IgG are most similar to each other. FIG. 6 shows a sequence alignment of the six murine antibody heavy and light chain variable region sequences, as well as the sequence for humanized h2A2 (derived from m2A2), as well as a depiction of a computer generated consensus sequence. In CDR1 of the heavy chain variable region, each of the antibodies comprise 10 amino acids comprising a Gly in the 1st position from the N-terminal, a Tyr or Phe in the 2nd position from the N-terminal, a Phe or Leu in the 4th position from the N-terminal, and a Thr or Ser in the 5th position from the N-terminal and a His or Asn in the 10th position from the N-terminal. In CDR2 of the heavy chain variable region, each of the antibodies comprise 16-17 amino acids comprising a Asn or Ile in the 2nd position from the N-terminal, a Phe or Ser in the 4th position from the N-terminal, a Thr in the 9th position from the C-terminal, a Tyr in the 7th position from the C-terminal, an Asn or Arg in the 6th position from the C-terminal, a Lys or Ala in the 4th position from the C-terminal and a Phe in the 3rd position from the C-terminal. In CDR3 of the heavy chain variable region of the murine antibodies, each of the antibodies comprise 7 to 11 amino acids comprising a Tyr or Thr at the 4th position from the N-terminal. In CDR1 of the light chain variable region, each of the antibodies comprise 10-16 amino acids comprising an Ala or Ser in the 2nd position from the N-terminal, a Ser in the 3rd position from the N-terminal, a Ser or Asp in the 5th position from the N-terminal, and a Tyr, Ser or Phe in the 3rd position from the C-terminal. In CDR2 of the light chain variable region, each of the antibodies comprise 7 amino acids comprising a Ser or Asn in the 3rd position from the N-terminal, a Lys or Ser in the 5th position from the N-terminal and a Ser or Asp in the 7th position from the N-terminal. In CDR3 of the light chain variable region, each of the murine antibodies comprise 9 amino acids comprising a Gln, Leu or Trp in the 1st position from the N-terminal, a Gln in the 2nd position from the N-terminal, a Pro in the 7th position from the N-terminal and a Thr in the 9th position from the N-terminal.

Also shown in FIG. 6 are anti-ceramide consensus sequence heavy chain and light chain CDRs based upon the sequence information derived from the CDR sequences of 6B5, 6C8, 7B10, 9H10 and 9H11. The present inventors have surprisingly found that the CDR regions of the light and heavy chain variable regions of the anti-ceramide antibodies have certain conserved amino acid residues. In some embodiments, a consensus sequence determined from the sequence of two or more of the anti-ceramide antibodies 6B5, 6C8, 7B10, 9H10, 9H11 and 2A2 can be used to generate an scFv antibody comprising consensus CDRs, consensus variable regions, or variable regions comprising at least about 80%, 90% or 95% sequence identitiy with a consensus variable region sequence.

Example 3: Generation of Anti-Ceramide scFv

Based on Mab efficacy data, the CDRs of 6B5 were chosen (along with 2a2) to be engineered into a single-chain Fv. Two single chain (sc) Fv constructs were engineered to express the scFv and provide purified scFv for efficacy testing. 6B5 scFv was readily expressed and purified. Biologic testing of scFv, as with Mabs, was performed using in vitro inhibition of Jurkat cell apoptosis and in vivo inhibition of Radiation GI Syndrome. FIG. 5 shows that 6B5 IgG protects against crypt death via the microcolony assay. FIG. 7 shows scFv inhibits jurkat cell apoptosis. FIG. 8 shows that 6B5 scFv protects against GI crypt depletion in vivo when administered 15 minutes prior to 15 Gy exposure. FIG. 9 shows that 6B5 scFv mitigates against GI crypt depletion in vivo when administered 24 hours after 15 Gy exposure.

Anti-Ceramide scFv Protects Mice from Lethal Acute Graft-Versus-Host Disease

C57BL/6 mice (MHC H2^(b) haplotype) were administered saline, 50 mg/kg humanized anti-ceramide h2A2 or 7.5 mg/kg anti-ceramide scFv 6B5 via the indicated route of administration and dosing schedule. Dosing began 15 min prior to 1100 cGy split-dose total-body irradiation (TBI). Mice subsequently received an allogeneic bone marrow transplantation 16-20 hours post TBI consisting of 5×10⁶ allogeneic bone marrow (BM) or BM and 2×10⁶ allogeneic CDS+ naïve T cells from B10.BR donor mice (MHC H2^(k2) haplotype). Mice were monitored daily for survival. Data represents Day 10 survival, determined to be representative of 90 day survival. An intravenous route of administration with saline on a dosing schedule of 0, 4, and 8 days resulted in 30% survival after 10 days. An intravenous route of administration with h2A2 monoclonal antibody on a dosing schedule of 0, 4, and 8 days resulted in 100% survival after 10 days (p<0.001 vs. saline control). An intravenous route of administration with scFv on a dosing schedule of 0, 4, and 8 days resulted in 60% survival after 10 days (p<0.05 vs. saline control). A subcutaneous route of administration with saline on a dosing schedule of 0, 2, 4, 6 and 8 days resulted in 0% survival after 10 days. A subcutaneous route of administration with saline on a dosing schedule of 0, 2, 4, 6 and 8 days resulted in 100% survival after 10 days (p<0.001 vs. saline control).

As shown in FIG. 10 , anti-ceramide scFV protects intestinal crypts in a dose-dependent manner. As shown in FIG. 11 , anti-ceramide scFv retains efficacy when administered via alternative injections. As shown in FIG. 12 , anti-ceramide h2A2 and scFv protect and mitigate the lethal effects of Radiation GI Syndrome. As shown in FIG. 13 , anti-ceramide scFv protects mice from lethal acute graft-versus-host disease. As shown in FIG. 14 , anti-ceramide scFv protects mouse intestinal stem cells during lethal acute graft-versus-host disease. As shown in FIG. 15 , anti-ceramide h2A2 and scFv increase retention of CD4+and CD8+lymphocytes within the mesentery lymph nodes (FIG. 15 ).

The above description is for the purpose of teaching the person of ordinary skill in the art how to practice the present invention, and it is not intended to detail all those obvious modifications and variations of it which will become apparent to the skilled worker upon reading the description. It is intended, however, that all such obvious modifications and variations be included within the scope of the present invention, which is defined by the following claims. The claims are intended to cover the components and steps in any sequence which is effective to meet the objectives there intended, unless the context specifically indicates the contrary. 

What is claimed is:
 1. A method of inhibiting apoptosis in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of an anti-ceramide antibody or antigen-binding fragment comprising a variable heavy chain (V_(H)) and a variable light chain (V_(L)), wherein the V_(H) comprises a heavy chain variable region CDR1 comprising the sequence GYTFTDHTIH (SEQ ID NO: 1), a heavy chain variable region CDR2 comprising the sequence YNYPRDGSTKYNEKFKG (SEQ ID NO: 2), and a heavy chain variable region CDR3 comprising the sequence GFITTVVPSAY (SEQ ID NO: 3), and the V_(L) comprises a light chain variable region CDR1 comprising the sequence RASKSISKYLA (SEQ ID NO: 4), a light chain variable region CDR2 comprising the sequence SGSTLQS (SEQ ID NO: 5), and a light chain variable region CDR3 comprising the sequence QQHNEYPWT (SEQ ID NO: 6). 